Align isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate CCNA_01841 CCNA_01841 isocitrate lyase
Query= BRENDA::P9WKK7 (428 letters) >FitnessBrowser__Caulo:CCNA_01841 Length = 539 Score = 151 bits (382), Expect = 4e-41 Identities = 133/450 (29%), Positives = 194/450 (43%), Gaps = 115/450 (25%) Query: 64 EWVNALGALTGNMAVQQVRAGLKA--------IYLSGWQVAGDANLSGHTYPDQSLYPAN 115 ++ +LG +G A Q ++A + +YLSGW VAG N GH PDQS++ Sbjct: 68 KFTQSLGCWSGFHAQQMIKAVKRLRGTTKGAYVYLSGWMVAGLRNRFGHL-PDQSMHEKT 126 Query: 116 SVPQVVRRINNALQRADQIA----------------------KIEGDTSVENWLAPIVAD 153 SV ++ I +L++AD++A I+ + E + PI+AD Sbjct: 127 SVVDLIEEIYVSLRQADEVAINDLFKALSAARKAGDQIAEQAAIKAIDNFETHVVPIIAD 186 Query: 154 GEAGFGGALNVYELQKALIAAGVAGSHWEDQLASEKKCGHLGGKVLIPTQQHIRTLTSAR 213 +AGFG Y L K +I AG E+Q++ K+CGH GKV +P + I L + R Sbjct: 187 IDAGFGNEHATYLLAKEMIKAGACCLQIENQVSDAKQCGHQDGKVTVPREDFIEKLRACR 246 Query: 214 LAADVADVPT-VVIARTDAEAATL------------ITSDVDE----------------- 243 LA + V V++ARTD+ A L + SD + Sbjct: 247 LAFEELGVDDGVIVARTDSLGAGLTQKIPVSQEPGDLASDYIKWLKTEPVTPENPLKDGE 306 Query: 244 ----RDQPFITGERTREGFYRTKNG------IEPCIARAKAYAPFADLIWMETGTPDLEA 293 +D F+ R G + ++G IE CIA ADL+W+ET TP+++ Sbjct: 307 LAIMKDGAFVKPVRMPNGLFAFQDGTGRQRVIEDCIANLTQGG--ADLLWIETDTPNVDE 364 Query: 294 ARQFSEAVKAEYPDQMLAYNCSPSFNW----------------KKHLD------------ 325 V+ P+ L YN SPSFNW K H D Sbjct: 365 IASMVAEVRRVVPNAKLTYNNSPSFNWTLNLRKQVRDQWIAEGKIHKDSYPDGNALMSAE 424 Query: 326 ----------DATIAKFQKELAA-MGFKFQFITLAGFHALNYSMFDLAYGY-AQNQMSAY 373 D +A+FQ ++AA G ITL FH S+ +L+ GY +++M AY Sbjct: 425 YDKSDLGREADERLARFQVDIAARAGVFHNLITLPTFHLTAKSVDELSRGYFGEDRMQAY 484 Query: 374 VELQEREFAAEERGYTATKHQREVGAGYFD 403 V +RE RG +A KHQ EVG+ D Sbjct: 485 VNTVQRE--EIRRGVSAVKHQHEVGSDLGD 512 Lambda K H 0.316 0.130 0.384 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 565 Number of extensions: 37 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 428 Length of database: 539 Length adjustment: 34 Effective length of query: 394 Effective length of database: 505 Effective search space: 198970 Effective search space used: 198970 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory